This hews more toward professional etiquette than language and usage, but I'll suggest that the most productive direction is to maintain the rhetorical high road in such communication.
What is it that you wish to accomplish?
- Is it to keep the door open for a possible future opportunity?
- Is it to let the other person know that you are angry?
- Is it to make the other person feel guilty about having disappointed you?
You will need to choose your words to suit your objective.
Assuming the first case, I might write,
Peter - I am sorry that you were not able to give my application the serious consideration I felt that it merited. I think that the time and energy that I put into the application showed my interest, and I hope you will understand that was disappointed by its reception. I would welcome your feedback, in hope of a better outcome next time.
Frankly, it is very easy to move and ignore an angry person, so unless I am in a position to make and carry out dire threats, I would not let such a person know of my anger.
I also think that there's very little to be gained by the third option. If he's a good person, "Peter" will probably remain convinced that he handled your application correctly, no matter how much you carry on. If he's a schmuck, he won't care that you're upset.